Model Checking Biological Systems Described Using Ambient Calculus

  • Radu Mardare
  • Corrado Priami
  • Paola Quaglia
  • Oleksandr Vagin
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3082)


We propose a way of performing model checking analysis for biological systems. The technics were developed for a CTL* logic built upon Ambient Calculus.

We introduce labeled syntax trees for ambient processes and use them as possible worlds in a Kripke structure developed for a propositional branching temporal logic. The accessibility relation over labeled syntax trees is generated by the reduction over corresponding Ambient Calculus processes.

Providing the algorithms for calculating the accessibility relation between states, we open the perspective of using model checking algorithms developed for temporal logics in analyzing any phenomena described in Ambient Calculus.


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  1. 1.
    HyTech: The HYbrid TECHnology Tool,
  2. 2.
    NuSMV: A new symbolic model checker,
  3. 3.
    Receptors directly activating trimetric g proteins,
  4. 4.
  5. 5.
  6. 6.
    Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., Walter, P.: Molecular Biology of the Cell, 4th edn., Garland Publishing, Inc. (2002)Google Scholar
  7. 7.
    Regev, A., Panina, E.M., Silverman, W., Cardelli, L., Shapiro, E.: Bioambients: An abstraction for biological compartments. Theoretical Computer Science (to appear, 2003),
  8. 8.
    Barwise, J., Moss, L.: Vicious Circles. On the Mathematics of Non-Wellfounded Phenomena. In: CLSI Lecture Notes, vol. 60, CSLI Publication, Stanford (1996)Google Scholar
  9. 9.
    Cardelli, L.: Brane calculi,
  10. 10.
    Cardelli, L., Caires, L.: A spatial logic for concurrency (part i). Information and Computation 186/2, 194–235 (2003)zbMATHGoogle Scholar
  11. 11.
    Cardelli, L., Gordon, A.D.: Ambient logic. Mathematical Structures in Computer Science (to appear),
  12. 12.
    Cardelli, L., Gordon, A.D.: Anytime, anywhere. modal logics for mobile ambients. In: Proceedings of the 27th ACM Symposium on Principles of Programming Languages, pp. 365–377 (2000)Google Scholar
  13. 13.
    Cardelli, L., Gordon, A.D.: Mobile ambients. In: Le Metayer, D. (ed.) Theoretical Computer Science, pp. 177–213 (June 2000) (Special Issue on Coordination)Google Scholar
  14. 14.
    Emerson, E.A.: Temporal and modal logic. In: Handbook of Theoretical Computer Science, B: Formal Models and Sematics, pp. 995–1072 (1990)Google Scholar
  15. 15.
    Mardare, R., Priami, C.: Computing the accessibility relation for ambient calculus. Technical report, Dipartimento di Informatica e Tlc, University of Trento (2003) (following the link Publications), Available at:
  16. 16.
    Mardare, R., Priami, C.: A propositional branching temporal logic for the ambient calculus. Technical report, Dipartimento di Informatica e Tlc, University of Trento (2003) (following the link Publications), Available at:

Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Radu Mardare
    • 1
  • Corrado Priami
    • 1
  • Paola Quaglia
    • 1
  • Oleksandr Vagin
    • 1
  1. 1.Dipartimento di Informatica e TelecomunicazioniUniversità di TrentoItaly

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